In the last ten years, green fluorescent protein (GFP) has changed from a nearly unknown protein to a frequently used tool in molecular biology, medicine and cell biology. The most common uses of GFP are as a fusion tag to visualize dynamic cellular events and to monitor protein localization, and as a report gene to monitor gene expression. GFP is commonly used in medicinal research. For example, GFP has been used as a marker for tumor cells, to illuminate tumor progression and allow for detection of metastases down to the single cell level.Computational methods will be used to investigate the following phenomena: * Yellow Fluorescent Proteins are GFP mutants that have lower fluorescent quantum yields than GFP's. The conformational freedom of the chromophore might be responsible for the lower quantum yields. * Mature GFP; i.e. fully fluorescent GFP, is most efficiently formed at temperatures well below 37xC. Computational methods will be used to search for mutants that mature more efficiently at higher temperatures and to establish the mechanism of their action. * GFP has an 11-sheet beta-barrel structure. Water and halide ions can enter the barrel. The pathways into the barrel can be found with activated molecular dynamics. The resultant information could be used to design more specific halide ion sensors. * DsRed is a red-emitting fluorescent protein from discosoma that is commercially available and has been studied in some detail. Two of the largest disadvantages of DsRed are its slow chromophore formation and the fact that DsRed is an obligate tetramer. These drawbacks could be overcome by computationally designing DsRed mutants that do not form multimeric structures, or by designing GFP mutants that can form chromophores with extended conjugation such as that found in DsRed. * The autocatalytic chromophore forming reaction of the purple GFP-like protein from Anemonia sulcata is significantly different to that observed in GFP. Computational methods will be used to investigate structural aspects of the chromophore formation in the purple GFP-Iike protein.